Engineered Cells Expressing Anti-Viral T Cell Receptors and Methods of Use Thereof

ABSTRACT

Provided herein are compositions comprising recombinant mammalian cells that express recombinant T cell rectors with specificity against EBV or CMV peptide:MHC antigens. Also provided are therapeutic methods of using the recombinant mammalian cells as cell therapies against viral infections.

1. CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of Ser. No. 17/480,697, filed Sep.21, 2021, which is a continuation of PCT/US2020/024028, filed Mar. 20,2020, which claims the benefit of U.S. Provisional Application No.62/821,808, filed Mar. 21, 2019, each of which is hereby incorporated inits entirety by reference.

2. SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically via Patent Center in ST.26 XML format and ishereby incorporated by reference in its entirety. Said XML copy, createdon Nov. 22, 2022, is named 53025US XML sequence listing.xml and is99,227 bytes in size.

3. FIELD

Provided herein are T cell receptors (TCRs) with binding specificity forEpstein-Barr Virus (EBV) or Cytomegalovirus (CMV) and compositionscomprising such TCRs, including non-natural DNA vectors encoding TCRs,pharmaceutical compositions, and non-natural cell therapies.

4. BACKGROUND

Human cytomegalovirus (CMV), or human herpesvirus-5 (HHV-5) is the typespecies of the virus genus Cytomegalovirus, which in turn is a member ofthe viral family known as Herpesviridae or herpesviruses. It is alsocommonly called CMV. HCMV infection is typically unnoticed in healthypeople, but can be life-threatening for the immunocompromised, such asHIV-infected persons, organ transplant recipients, or newborn infants.Congenital cytomegalovirus infection can lead to significant morbidityand even death. After infection, HCMV remains latent within the bodythroughout life and can be reactivated at any time. Eventually, it maycause mucoepidermoid carcinoma and possibly other malignancies such asprostate cancer.

Ganciclovir (Cytovene) treatment is used as CMV therapy for people withdepressed immunity who have either sight-related or life-threateningillnesses. Valganciclovir (Valcyte) is also effective CMV therapy and isgiven orally: it is a pro-drug that gets converted into ganciclovir inthe body, but is much better absorbed orally than the latter. Thetherapeutic effectiveness is frequently compromised by the emergence ofdrug-resistant virus isolates. Foscarnet or cidofovir are only given topeople with CMV resistant to ganciclovir, because foscarnet has notablenephrotoxicity, resulting in increased or decreased Ca2+ or P, anddecreased Mg2+. There remains an opportunity to develop more efficacioustherapies for CMV infections.

The Epstein—Barr virus (EBV), formally called Human gammaherpesvirus 4,is one of eight known human herpesvirus types in the herpes family, andis one of the most common viruses in humans.

It is best known as the cause of infectious mononucleosis (“mono” or“glandular fever”). It is also associated with various non-malignant,premalignant, and malignant Epstein-Barr virus-associatedlymphoproliferative diseases such as Burkitt lymphoma, hemophagocyticlympohistiocytosis, and Hodgkin's lymphoma; non-lymphoid malignanciessuch as gastric cancer and nasopharyngeal carcinoma; and conditionsassociated with human immunodeficiency virus such as hairy leukoplakiaand central nervous system lymphomas. The virus is also associated withthe childhood disorders of Alice in Wonderland Syndrome and acutecerebellar ataxia and, based on some evidence, higher risks ofdeveloping certain autoimmune diseases, especially dermatomyositis,systemic lupus erythematosus, rheumatoid arthritis, Sjögren's syndrome,and multiple sclerosis. About 200,000 cancer cases per year are thoughtto be attributable to EBV.

Infection with EBV occurs by the oral transfer of saliva and genitalsecretions. Most people become infected with EBV and gain adaptiveimmunity. In the United States, about half of all five-year-old childrenand about 90% of adults have evidence of previous infection. Infantsbecome susceptible to EBV as soon as maternal antibody protectiondisappears. Many children become infected with EBV, and these infectionsusually cause no symptoms or are indistinguishable from the other mild,brief illnesses of childhood. In the United States and other developedcountries, many people are not infected with EBV in their childhoodyears. When infection with EBV occurs during adolescence, it causesinfectious mononucleosis 35 to 50% of the time.

Currently, there are no drugs available for treatment or prevention ofEBV infections. There remains a need and opportunity to develop anti-EBVtherapeutics.

5. SUMMARY

Provided herein are novel TCRs with binding specificity for EBV or CMV.

Also provided are isolated polynucleotides encoding the TCRs providedherein, and portions thereof.

Also provided are vectors comprising such polynucleotides.

Also provided are recombinant host cells comprising such polynucleotidesand recombinant host cells comprising such vectors.

Also provided are methods of producing the TCRs using thepolynucleotides, vectors, or host cells provided herein.

Also provided are pharmaceutical compositions comprising the TCRs and apharmaceutically acceptable excipient.

In some aspects, the present invention provides a pharmaceuticalcomposition comprising the TCR and an excipient. In some embodiments,the TCR is in an amount sufficient as prophylaxis against infectiousdisease when administered to a subject. In some embodiments, the TCR isan amount sufficient to clear infectious disease in an individualactively fighting infection.

In other aspects, the present invention provides a method of treating adisease comprising the step of: administering an effective amount of theTCR or the pharmaceutical composition provided herein to a subject withthe disease.

In some aspects, the present invention provides a mixture ofpolynucleotides encoding the TCRs provided herein. In other aspects, thepresent invention provides a mixture of vectors comprising the isolatedpolynucleotides. In other aspects, the present invention provides amixture of host cell clones comprising the mixture of polynucleotides orvectors.

Some aspects of the present invention are related to a method ofproducing TCR, comprising: expressing the antibodies in host cells usinga library of polynucleotide vectors, and isolating the cells thatexpress the TCR.

TCRs of the invention may be transformed into T cells, rendering themcapable of destroying cells presenting CMV or EBV peptide antigens, foradministration to a patient in the treatment process known as adoptivetherapy (see Zhao et al., (2007) J Immunol. 179: 5845-54; Robbins etal., (2008) J Immunol. 180:6 116-31; and WO2008/038002).

In other aspects, the present invention provides methods for discoveryof TCRs from highly diverse mammalian T cell repertoires.

6. BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 summarizes the method of discovering TCRs from transcriptsexpressed in peripheral blood TCRs isolated from virus seropositivehuman donors.

FIG. 2 summarizes a method of encapsulating T cells into physicalcontainers with lysis mix and solid supports that capture nucleic acidtargets from lysed cells.

FIG. 3 summarizes a method of encapsulating target-specific primers withnucleic acid targets affixed to solid supports.

FIG. 4 shows the method of amplifying individual target nucleic acidswith complementary regions.

FIG. 5 shows the individual amplified target nucleic acids withcomplementary regions.

FIG. 6 summarizes a method of fusing separate amplified nucleic acidtargets into single fused nucleic acid constructs.

FIG. 7 shows the method of generating circularized gene expressionconstructs from the fused nucleic acid constructs.

7. DETAILED DESCRIPTION 7.1. Definitions

Unless otherwise defined herein, scientific and technical terms used inconnection with the present invention shall have the meanings that arecommonly understood by those of ordinary skill in the art. Further,unless otherwise required by context, singular terms shall includepluralities and plural terms shall include the singular. Generally,nomenclatures used in connection with, and techniques of, cell andtissue culture, molecular biology, immunology, microbiology, geneticsand protein and nucleic acid chemistry and hybridization describedherein are those well-known and commonly used in the art. The methodsand techniques of the present invention are generally performedaccording to conventional methods well known in the art and as describedin various general and more specific references that are cited anddiscussed throughout the present specification unless otherwiseindicated. See, e.g., Sambrook et al. Molecular Cloning: A LaboratoryManual, 2d ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y. (1989) and Ausubel et al., Current Protocols in Molecular Biology,Greene Publishing Associates (1992), and Harlow and Lane Antibodies: ALaboratory Manual Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y. (1990), which are incorporated herein by reference.Enzymatic reactions and purification techniques are performed accordingto manufacturer's specifications, as commonly accomplished in the art oras described herein. The terminology used in connection with, and thelaboratory procedures and techniques of, analytical chemistry, syntheticorganic chemistry, and medicinal and pharmaceutical chemistry describedherein are those well-known and commonly used in the art. Standardtechniques can be used for chemical syntheses, chemical analyses,pharmaceutical preparation, formulation, and delivery, and treatment ofpatients.

The following terms, unless otherwise indicated, shall be understood tohave the following meanings:

The term “T cell receptor”, or “TCR”, is a molecule found on the surfaceof T cells, or T lymphocytes, that is responsible for recognizingfragments of antigen as peptides bound to major histocompatibilitycomplex (MHC) molecules. The TCR is composed of two different proteinchains (that is, it is a heterodimer). In humans, in 95% of T cells theTCR consists of an alpha (α) chain and a beta (β) chain (encoded by TRAand TRB, respectively), whereas in 5% of T cells the TCR consists ofgamma and delta (γ/δ) chains (encoded by TRG and TRD, respectively).This ratio changes during ontogeny and in diseased states (such asleukemia). It also differs between species. Each locus can produce avariety of polypeptides with constant and variable regions. When the TCRengages with antigenic peptide and MHC (peptide:MHC), the T lymphocyteis activated through signal transduction, that is, a series ofbiochemical events mediated by associated enzymes, co-receptors,specialized adaptor molecules, and activated or released transcriptionfactors. The TCR is a disulfide-linked membrane-anchored heterodimericprotein normally consisting of the highly variable alpha (α) and beta(β) chains expressed as part of a complex with the invariant CD3 chainmolecules. T cells expressing this receptor are referred to as α:β (orαβ) T cells, though a minority of T cells express an alternate receptor,formed by variable gamma (γ) and delta (δ) chains, referred as γδ Tcells. Each chain is composed of two extracellular domains: Variable (V)region and a Constant (C) region, both of Immunoglobulin superfamily(IgSF) domain forming antiparallel β-sheets. The Constant region isproximal to the cell membrane, followed by a transmembrane region and ashort cytoplasmic tail, while the Variable region binds to thepeptide/MHC complex. The variable domain of both the TCR α-chain andβ-chain each have three hypervariable or complementarity determiningregions (CDRs). There is also an additional area of hypervariability onthe β-chain (HV4) that does not normally contact antigen and, therefore,is not considered a CDR. The residues in these variable domains arelocated in two regions of the TCR, at the interface of the α- andβ-chains and in the β-chain framework region that is thought to be inproximity to the CD3 signal-transduction complex. CDR3 is the main CDRresponsible for recognizing processed antigen, although CDR1 of thealpha chain has also been shown to interact with the N-terminal part ofthe antigenic peptide, whereas CDR1 of the β-chain interacts with theC-terminal part of the peptide. CDR2 is thought to recognize the MHC.CDR4 of the β-chain is not thought to participate in antigenrecognition. The constant domain of the TCR consists of short connectingsequences in which a cysteine residue forms disulfide bonds, which forma link between the two chains. The generation of TCR diversity issimilar to that for antibodies and B cell antigen receptors. It arisesmainly from genetic recombination of the DNA encoded segments inindividual somatic T cells by somatic V(D)J recombination using RAG1 andRAG2 recombinases. Unlike immunoglobulins, TCR genes do not undergosomatic hypermutation. Each recombined TCR possess unique antigenspecificity, determined by the structure of the antigen-binding siteformed by the α and β chains in case of αβ T cells or γ and δ chains oncase of γδ T cells.

“Affinity” refers to the strength of the sum total of non-covalentinteractions between a single binding site of a molecule (e.g., an RPP)and its binding partner (e.g., an antigen or epitope). Unless indicatedotherwise, as used herein, “affinity” refers to intrinsic bindingaffinity, which reflects a 1:1 interaction between members of a bindingpair (e.g., TCR and peptide:MHC). The affinity of a molecule X for itspartner Y can be represented by the dissociation equilibrium constant(K_(D)). The kinetic components that contribute to the dissociationequilibrium constant are described in more detail below. Affinity can bemeasured by common methods known in the art, including those describedherein. Affinity can be determined, for example, using surface plasmonresonance (SPR) technology (e.g., BIACORE®) or biolayer interferometry(e.g., FORTEBIO®).

“Avidity” refers to the accumulated strength of multiple affinities ofindividual non-covalent binding interactions, such as between a proteinreceptor and its ligand, and is commonly referred to as functionalaffinity. As such, avidity is distinct from affinity, which describesthe strength of a single interaction. However, because individualbinding events increase the likelihood of other interactions to occur(i.e. increase the local concentration of each binding partner inproximity to the binding site), avidity should not be thought of as themere sum of its constituent affinities but as the combined effect of allaffinities participating in the biomolecular interaction.

The “major histocompatibility complex” (MHC) is a set of cell surfaceproteins essential for the acquired immune system to recognize foreignmolecules in vertebrates, which in turn determines histocompatibility.The main function of MHC molecules is to bind to antigens derived frompathogens and display them on the cell surface for recognition by theappropriate T-cells. The MHC determines compatibility of donors fororgan transplant, as well as one's susceptibility to an autoimmunedisease via crossreacting immunization. The human MHC is also called theHLA (human leukocyte antigen) complex (often just the HLA).

“MHC class I” molecules are one of two primary classes of MHC moleculesand are found on the cell surface of all nucleated cells in the bodiesof jawed vertebrates. They also occur on platelets, but not on red bloodcells. Their function is to display peptide fragments of proteins fromwithin the cell to cytotoxic T cells, often termed “peptide:MHC”; thiswill trigger an immediate response from the immune system against aparticular non-self antigen displayed with the help of an MHC class Iprotein. Because MHC class I molecules present peptides derived fromcytosolic proteins, the pathway of MHC class I presentation is oftencalled cytosolic or endogenous pathway.

With regard to the binding of an TCR to a target peptide:MHC, the terms“bind,” “specific binding,” “specifically binds to,” “specific for,”“selectively binds,” and “selective for” a particular antigen (e.g., apolypeptide target) or an epitope on a particular antigen mean bindingthat is measurably different from a non-specific or non-selectiveinteraction (e.g., with a non-target molecule). Specific binding can bemeasured, for example, by measuring binding to a target molecule andcomparing it to binding to a non-target molecule. Specific binding canalso be determined by competition with a control molecule that mimicsthe epitope recognized on the target molecule. In that case, specificbinding is indicated if the binding of the RPP to the target molecule iscompetitively inhibited by the control molecule.

Percent “identity” between a polypeptide sequence and a referencesequence, is defined as the percentage of amino acid residues in thepolypeptide sequence that are identical to the amino acid residues inthe reference sequence, after aligning the sequences and introducinggaps, if necessary, to achieve the maximum percent sequence identity.Alignment for purposes of determining percent amino acid sequenceidentity can be achieved in various ways that are within the skill inthe art, for instance, using publicly available computer software suchas BLAST, BLAST-2, ALIGN, MEGALIGN (DNASTAR), CLUSTALW, CLUSTAL OMEGA,or MUSCLE software. Those skilled in the art can determine appropriateparameters for aligning sequences, including any algorithms needed toachieve maximal alignment over the full length of the sequences beingcompared.

A “conservative substitution” or a “conservative amino acidsubstitution,” refers to the substitution an amino acid with achemically or functionally similar amino acid. Conservative substitutiontables providing similar amino acids are well known in the art. By wayof example, the groups of amino acids provided in TABLES 1-3 are, insome embodiments, considered conservative substitutions for one another.

TABLE 1 Selected groups of amino acids that are considered conservativesubstitutions for one another, in certain embodiments. Acidic Residues Dand E Basic Residues K, R, and H Hydrophilic Uncharged Residues S, T, N,and Q Aliphatic Uncharged Residues G, A V, L, and I Non-polar UnchargedResidues C, M, and P Aromatic Residues F, Y, and W

TABLE 2 Additional selected groups of amino acids that are consideredconservative substitutions for one another, in certain embodiments.Group 1 A, S, and T Group 2 D and E Group 3 N and Q Group 4 R and KGroup 5 I, L, and M Group 6 F, Y, and W

TABLE 3 Further selected groups of amino acids that are consideredconservative substitutions for one another, in certain embodiments.Group A A and G Group B D and E Group C N and Q Group D R, K, and HGroup E I, L, M, V Group F Y and W Group G S and T Group H C and M

Additional conservative substitutions may be found, for example, inCreighton, Proteins: Structures and Molecular Properties 2nd ed. (1993)W. H. Freeman & Co., New York, N.Y. An RPP generated by making one ormore conservative substitutions of amino acid residues in a parent RPPis referred to as a “conservatively modified variant.”

The term “treating” (and variations thereof such as “treat” or“treatment”) refers to clinical intervention in an attempt to alter thenatural course of a disease or condition in a subject in need thereof.Treatment can be performed both for prophylaxis and during the course ofclinical pathology. Desirable effects of treatment include preventingoccurrence or recurrence of disease, alleviation of symptoms, diminishof any direct or indirect pathological consequences of the disease,preventing metastasis, decreasing the rate of disease progression,amelioration or palliation of the disease state, and remission orimproved prognosis.

As used herein, the term “therapeutically effective amount” or“effective amount” refers to an amount of an RPP or pharmaceuticalcomposition provided herein that, when administered to a subject, iseffective to treat a disease or disorder.

As used herein, the term “subject” means a mammalian subject. Exemplarysubjects include humans, monkeys, dogs, cats, mice, rats, cows, horses,camels, goats, rabbits, and sheep. In certain embodiments, the subjectis a human. In some embodiments the subject has a disease or conditionthat can be treated with an RPP provided herein. In some aspects, thedisease or condition is a cancer. In some aspects, the disease orcondition is a viral infection.

The term “package insert” is used to refer to instructions customarilyincluded in commercial packages of therapeutic or diagnostic products(e.g., kits) that contain information about the indications, usage,dosage, administration, combination therapy, contraindications and/orwarnings concerning the use of such therapeutic or diagnostic products.

A “chemotherapeutic agent” refers to a chemical compound useful in thetreatment of cancer. Chemotherapeutic agents include “anti-hormonalagents” or “endocrine therapeutics” which act to regulate, reduce,block, or inhibit the effects of hormones that can promote the growth ofcancer.

The term “pharmaceutical composition” refers to a preparation which isin such form as to permit the biological activity of an activeingredient contained therein to be effective in treating a subject, andwhich contains no additional components which are unacceptably toxic tothe subject.

The terms “modulate” and “modulation” refer to reducing or inhibitingor, alternatively, activating or increasing, a recited variable.

The terms “increase” and “activate” refer to an increase of 10%, 20%,30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 2-fold, 3-fold,4-fold, 5-fold, 10-fold, 20-fold, 50-fold, 100-fold, or greater in arecited variable.

The terms “reduce” and “inhibit” refer to a decrease of 10%, 20%, 30%,40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 2-fold, 3-fold, 4-fold,5-fold, 10-fold, 20-fold, 50-fold, 100-fold, or greater in a recitedvariable.

The term “effector T cell” includes T helper (i.e., CD4+) cells andcytotoxic (i.e., CD8+) T cells. CD4+ effector T cells contribute to thedevelopment of several immunologic processes, including maturation of Bcells into plasma cells and memory B cells, and activation of cytotoxicT cells and macrophages. CD8+ effector T cells destroy virus-infectedcells and tumor cells. See Seder and Ahmed, Nature Immunol., 2003,4:835-842, incorporated by reference in its entirety, for additionalinformation on effector T cells.

The term “regulatory T cell” includes cells that regulate immunologicaltolerance, for example, by suppressing effector T cells. In someaspects, the regulatory T cell has a CD4+CD25+Foxp3+ phenotype. In someaspects, the regulatory T cell has a CD8+CD25+ phenotype. See Nocentiniet al., Br. J. Pharmacol., 2012, 165:2089-2099, incorporated byreference in its entirety, for additional information on regulatory Tcells.

A “cytotoxic T cell” (also known as TC, cytotoxic T lymphocyte, CTL,T-killer cell, cytolytic T cell, CD8+ T-cell or killer T cell) is a Tlymphocyte (a type of white blood cell) that kills cancer cells, cellsthat are infected (particularly with viruses), or cells that are damagedin other ways. Most cytotoxic T cells express T-cell receptors (TCRs)that can recognize a specific antigen. An antigen is a molecule capableof stimulating an immune response, and is often produced by cancer cellsor viruses. Antigens inside a cell are bound to class I MHC molecules,and brought to the surface of the cell by the class I MHC molecule,where they can be recognized by the T cell. If the TCR is specific forthat antigen, it binds to the complex of the class I MHC molecule andthe antigen, and the T cell destroys the cell.

The term “in vivo” translates to “in the living”, and refers toscientific studies in which the effects of various biological entitiesare tested on whole, living organisms or cells, usually animals,including humans, and plants, as opposed to a tissue extract or deadorganism. This is not to be confused with experiments done in vitro(“within the glass”), i.e., in a laboratory environment using testtubes, Petri dishes, etc. Examples of investigations in vivo include:the pathogenesis of disease by comparing the effects of bacterialinfection with the effects of purified bacterial toxins; the developmentof non-antibiotics, antiviral drugs, and new drugs generally; and newsurgical procedures. Consequently, animal testing and clinical trialsare major elements of in vivo research. In vivo testing is oftenemployed over in vitro because it is better suited for observing theoverall effects of an experiment on a living subject.

The term “recombinant” refers to proteins that result from theexpression of recombinant DNA within living cells. Recombinant DNA isthe general name for a piece of DNA that has been created by thecombination of at least two separate segments of DNA.

The term “in vitro” translates to “in the glass”, and refers toscientific studies that are performed with microorganisms, cells, orbiological molecules outside their normal biological context.Colloquially called “test-tube experiments”, these studies in biologyand its subdisciplines are traditionally done in labware such as testtubes, flasks, Petri dishes, and microtiter plates. Studies conductedusing components of an organism that have been isolated from their usualbiological surroundings permit a more detailed or more convenientanalysis than can be done with whole organisms; however, resultsobtained from in vitro experiments may not fully or accurately predictthe effects on a whole organism. In contrast to in vitro experiments, invivo studies are those conducted in animals, including humans, and wholeplants.

A “variant” of a polypeptide (e.g., an antibody) comprises an amino acidsequence wherein one or more amino acid residues are inserted into,deleted from and/or substituted into the amino acid sequence relative tothe native polypeptide sequence, and retains essentially the samebiological activity as the native polypeptide. The biological activityof the polypeptide can be measured using standard techniques in the art(for example, if the variant is an antibody, its activity may be testedby binding assays, as described herein). Variants of the inventioninclude fragments, analogs, recombinant polypeptides, syntheticpolypeptides, and/or fusion proteins.

A “derivative” of a polypeptide is a polypeptide (e.g., an antibody)that has been chemically modified, e.g., via conjugation to anotherchemical moiety such as, for example, polyethylene glycol, albumin(e.g., human serum albumin), phosphorylation, and glycosylation. Unlessotherwise indicated, the term “antibody” includes, in addition toantibodies comprising two full-length heavy chains and two full-lengthlight chains, derivatives, variants, fragments, and muteins thereof,examples of which are described below.

A nucleotide sequence is “operably linked” to a regulatory sequence ifthe regulatory sequence affects the expression (e.g., the level, timing,or location of expression) of the nucleotide sequence. A “regulatorysequence” is a nucleic acid that affects the expression (e.g., thelevel, timing, or location of expression) of a nucleic acid to which itis operably linked. The regulatory sequence can, for example, exert itseffects directly on the regulated nucleic acid, or through the action ofone or more other molecules (e.g., polypeptides that bind to theregulatory sequence and/or the nucleic acid). Examples of regulatorysequences include promoters, enhancers and other expression controlelements (e.g., polyadenylation signals). Further examples of regulatorysequences are described in, for example, Goeddel, 1990, Gene ExpressionTechnology: Methods in Enzymology 185, Academic Press, San Diego, Calif.and Baron et al., 1995, Nucleic Acids Res. 23:3605-06.

A “host cell” is a cell that can be used to express a nucleic acid,e.g., a nucleic acid of the invention Typically, a host cell is acultured cell that can be transformed or transfected with apolypeptide-encoding nucleic acid, which can then be expressed in thehost cell.

The phrase “recombinant host cell” can be used to denote a host cellthat has been transformed or transfected with a nucleic acid to beexpressed. A host cell also can be a cell that comprises the nucleicacid but does not express it at a desired level unless a regulatorysequence is introduced into the host cell such that it becomes operablylinked with the nucleic acid. It is understood that the term host cellrefers not only to the particular subject cell but to the progeny orpotential progeny of such a cell. Because certain modifications mayoccur in succeeding generations due to, e.g., mutation or environmentalinfluence, such progeny may not, in fact, be identical to the parentcell, but are still included within the scope of the term as usedherein.

“Cell therapy” (also called cellular therapy or cytotherapy) is therapyin which cellular material is injected, grafted or implanted into apatient; this generally means intact, living cells. For example, T cellscapable of fighting cancer cells via cell-mediated immunity may beinjected in the course of immunotherapy. A “TCR-T cell therapy” is atype of cellular therapy wherein at least one recombinant TCR sequenceis engineered into autologous or allogeneic T cells, and then theengineered TCR-T cells are injected into a patient. In suchapplications, the TCR is directed against a peptide:MHC of therapeuticinterest, for example, a virus peptide:MHC.

7.2. Other Interpretational Conventions

Ranges recited herein are understood to be shorthand for all of thevalues within the range, inclusive of the recited endpoints. Forexample, a range of 1 to 50 is understood to include any number,combination of numbers, or sub-range from the group consisting of 1, 2,3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42, 43, 44, 45, 46, 47, 48, 49, and 50.

Unless otherwise indicated, reference to a compound that has one or morestereocenters intends each stereoisomer, and all combinations ofstereoisomers, thereof.

7.3. Nucleic Acids

In one aspect, the present invention provides isolated nucleic acidmolecules. The nucleic acids comprise, for example, polynucleotides thatencode all or part of a TCR, for example, one or both chains of a TCR ofthe invention, or a fragment, derivative, mutein, or variant thereof.

In another aspect, the present invention provides methods to generatelibraries of nucleic acids that encode for libraries of TCRs, derivedfrom primary T cells. These libraries of nucleic acids are generated byisolating T cells into single-cell reaction containers, wherein they arelysed and TCR-specific nucleic acids are purified or captured, forexample on solid supports such as beads. The present invention providesmethods for performing capture of transcripts from millions of single Tcells in parallel. Capture of transcripts is followed by amplificationof nucleic acids that encode TCR alpha and beta, and subsequent linkageof said nucleic acids into libraries of fused constructs that encodeboth TCR alpha and beta. In such libraries the native pairing of TCRalpha and beta, as originally found in the input T cells, is maintained.Such methods are performed in parallel on millions of single T cells,such that the resulting library of fused TCR alpha and beta nucleicacids comprises natively paired sequences for millions of single cells.

7.4. Expression Vectors

The present invention provides vectors comprising a nucleic acidencoding a polypeptide of the invention or a portion thereof. Examplesof vectors include, but are not limited to, plasmids, viral vectors,non-episomal mammalian vectors and expression vectors, for example,recombinant expression vectors.

In another aspect of the present invention, expression vectorscontaining the nucleic acid molecules and polynucleotides of the presentinvention are also provided, and host cells transformed with suchvectors, and methods of producing the polypeptides are also provided.The term “expression vector” refers to a plasmid, phage, virus or vectorfor expressing a polypeptide from a polynucleotide sequence. Vectors forthe expression of the polypeptides contain at a minimum sequencesrequired for vector propagation and for expression of the cloned insert.An expression vector comprises a transcriptional unit comprising anassembly of (1) a genetic element or elements having a regulatory rolein gene expression, for example, promoters or enhancers, (2) a sequencethat encodes polypeptides and proteins to be transcribed into mRNA andtranslated into protein, and (3) appropriate transcription initiationand termination sequences. These sequences may further include aselection marker. Vectors suitable for expression in host cells arereadily available and the nucleic acid molecules are inserted into thevectors using standard recombinant DNA techniques. Such vectors caninclude promoters which function in specific tissues, and viral vectorsfor the expression of polypeptides in targeted human or animal cells.

The recombinant expression vectors of the invention can comprise anucleic acid of the invention in a form suitable for expression of thenucleic acid in a host cell. The recombinant expression vectors includeone or more regulatory sequences, selected on the basis of the hostcells to be used for expression, which is operably linked to the nucleicacid sequence to be expressed. Regulatory sequences include those thatdirect constitutive expression of a nucleotide sequence in many types ofhost cells (e.g., SV40 early gene enhancer, Rous sarcoma virus promoterand cytomegalovirus promoter), those that direct expression of thenucleotide sequence only in certain host cells (e.g., tissue-specificregulatory sequences, see Voss et al., 1986, Trends Biochem. Sci.11:287, Maniatis et al., 1987, Science 236:1237, incorporated byreference herein in their entireties), and those that direct inducibleexpression of a nucleotide sequence in response to particular treatmentor condition (e.g., the metallothionin promoter in mammalian cells andthe tet-responsive and/or streptomycin responsive promoter in bothprokaryotic and eukaryotic systems (see id.). It will be appreciated bythose skilled in the art that the design of the expression vector candepend on such factors as the choice of the host cell to be transformed,the level of expression of protein desired, etc. The expression vectorsof the invention can be introduced into host cells to thereby produceproteins or peptides, including fusion proteins or peptides, encoded bynucleic acids as described herein.

The invention further provides methods of making polypeptides. A varietyof other expression/host systems may be utilized. Vector DNA can beintroduced into prokaryotic or eukaryotic systems via conventionaltransformation or transfection techniques. These systems include but arenot limited to microorganisms such as bacteria (for example, E. coli)transformed with recombinant bacteriophage, plasmid or cosmid DNAexpression vectors; yeast transformed with yeast expression vectors;insect cell systems infected with virus expression vectors (e.g.,baculovirus); plant cell systems transfected with virus expressionvectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus,TMV) or transformed with bacterial expression vectors (e.g., Ti orpBR322 plasmid); or animal cell systems Mammalian cells useful inrecombinant protein production include but are not limited to VEROcells, HeLa cells, Chinese hamster ovary (CHO) cell lines, or theirderivatives such as Veggie CHO and related cell lines which grow inserum-free media (see Rasmussen et al., 1998, Cytotechnology 28:31) orCHO strain DX-B11, which is deficient in DHFR (see Urlaub et al., 1980,Proc. Natl. Acad. Sci. USA 77:4216-20) COS cells such as the COS-7 lineof monkey kidney cells (ATCC CRL 1651) (see Gluzman et al., 1981, Cell23:175), W138, BHK, HepG2, 3T3 (ATCC CCL 163), RIN, MDCK, A549, PC12,K562, L cells, C127 cells, BHK (ATCC CRL 10) cell lines, the CV1/EBNAcell line derived from the African green monkey kidney cell line CV1(ATCC CCL 70) (see McMahan et al., 1991, EMBO J. 10:2821), humanembryonic kidney cells such as 293, 293 EBNA or MSR 293, human epidermalA431 cells, human Colo205 cells, other transformed primate cell lines,normal diploid cells, cell strains derived from in vitro culture ofprimary tissue, primary explants, HL-60, U937, HaK or Jurkat cells, orany kind of primary cells, such as T cells Mammalian expression allowsfor the production of secreted or soluble polypeptides which may berecovered from the growth medium, or expression on the cell surface.

For stable transfection of mammalian cells, it is known that, dependingupon the expression vector and transfection technique used, only a smallfraction of cells may integrate the foreign DNA into their genome. Inorder to identify and select these integrants, a gene that encodes aselectable marker (e.g., for resistance to antibiotics) is generallyintroduced into the host cells along with the gene of interest. Oncesuch cells are transformed with vectors that contain selectable markersas well as the desired expression cassette, the cells can be allowed togrow in an enriched media before they are switched to selective media,for example. The selectable marker is designed to allow growth andrecovery of cells that successfully express the introduced sequences.Resistant clumps of stably transformed cells can be proliferated usingtissue culture techniques appropriate to the cell line employed. Anoverview of expression of recombinant proteins is found in Methods ofEnzymology, v. 185, Goeddell, D. V., ed., Academic Press (1990).Preferred selectable markers include those which confer resistance todrugs, such as G418, hygromycin and methotrexate. Cells stablytransfected with the introduced nucleic acid can be identified by drugselection (e.g., cells that have incorporated the selectable marker genewill survive, while the other cells die), among other methods. Thetransformed cells can be cultured under conditions that promoteexpression of the polypeptide.

In addition, the polypeptides can be synthesized in solution or on asolid support in accordance with conventional techniques. Variousautomatic synthesizers are commercially available and can be used inaccordance with known protocols. See, for example, Stewart and Young,Solid Phase Peptide Synthesis, 2d.Ed., Pierce Chemical Co. (1984); Tamet al., J Am Chem Soc, 105:6442, (1983); Merrifield, Science 232:341-347(1986); Barany and Merrifield, The Peptides, Gross and Meienhofer, eds,Academic Press, New York, 1-284; Barany et al., Int J Pep Protein Res,30:705-739 (1987).

The polypeptides and proteins of the present invention can be purifiedaccording to protein purification techniques well known to those ofskill in the art. These techniques involve, at one level, the crudefractionation of the proteinaceous and non-proteinaceous fractions.Having separated the peptide polypeptides from other proteins, thepeptide or polypeptide of interest can be further purified usingchromatographic and electrophoretic techniques to achieve partial orcomplete purification (or purification to homogeneity). The term“purified polypeptide” as used herein, is intended to refer to acomposition, isolatable from other components, wherein the polypeptideis purified to any degree relative to its naturally-obtainable state. Apurified polypeptide therefore also refers to a polypeptide that is freefrom the environment in which it may naturally occur. Generally,“purified” will refer to a polypeptide composition that has beensubjected to fractionation to remove various other components, and whichcomposition substantially retains its expressed biological activity.Where the term “substantially purified” is used, this designation willrefer to a peptide or polypeptide composition in which the polypeptideor peptide forms the major component of the composition, such asconstituting about 50%, about 60%, about 70%, about 80%, about 85%, orabout 90% or more of the proteins in the composition.

In some aspects, the present invention includes libraries ofTCR-encoding nucleic acid vectors for integration into mammaliangenomes. Such vectors include plasmids, retroviruses, and lentivirus.The libraries of nucleic acid vectors may include 10, 100, 1,000,10,000, or more than 100,000 different antibody-encoding sequences. Thesequences are derived from T cells. These libraries of nucleic acids aregenerated by isolating T cells into single-cell reaction containers,wherein they are lysed and antibody-specific nucleic acids are purifiedor captured, for example on solid supports such as beads. The presentinvention provides methods for performing capture of transcripts frommillions of single T cells in parallel. Capture of transcripts isfollowed by amplification of nucleic acids that encode TCR alpha andbeta, and subsequent linkage of said nucleic acids into libraries offused constructs that encode both TCR alpha and beta. In such librariesthe native pairing of TCR alpha and beta, as originally found in theinput T cells, is maintained Such methods are performed in parallel onmillions of single T cells, such that the resulting library of fused TCRalpha and beta nucleic acids comprises natively paired sequences formillions of single cells. These paired fused amplicons are thenengineered into full-length TCR constructs using Gibson Assembly,restriction endonucleases, or other recombinant DNA techniques.

Engineering into full-length TCR constructs is performed on the fulllibrary en masse, such that the TCR sequence content and TCR sequencecounts of the library are essentially maintained throughout the process.In some aspects, the library of expression vectors is engineered in twosteps, such that the TCR fragment amplicon is subcloned into anintermediate vector, and then a second round of Gibson Assembly,restriction digestion, or other recombinant technique is used toengineer additional domains of the antibody into the linker of the TCRfragment amplicon. The native pairing of TCR alpha and beta isessentially maintained throughout the process of engineering intofull-length expression vector libraries. The vectors are designed invarious orientations, for example, two separate promoters driveexpression of TCR alpha and beta, or one promoter drives expression ofboth TCR alpha and beta, and a translational skip motif is used toseparately translate the TCR alpha and beta into separate polypeptides.In some embodiments, the expression vectors comprise sequences forsite-directed integration into mammalian production cells, for example,CRISPR-Cas9, Flp-In, Cre/Lox, or zinc finger recombination methods.Site-directed integration ensures that each mammalian production cellencodes a single TCR alpha and beta sequence, and decreases variabilityin expression levels between single production cells.

7.5. T Cell Receptors

Native TCRs exist in heterodimeric αβ or γδ forms. However, recombinantTCRs consisting of aa or ββ homodimers have previously been shown tobind to peptide MHC molecules. Therefore, the TCR of the invention maybe a heterodimeric β TCR or may be an αα or ββ homodimeric TCR. For usein adoptive cell therapy, an b β heterodimeric TCR may, for example, betransfected as full-length chains having both cytoplasmic andtransmembrane domains. In certain embodiments TCRs of the invention mayhave an introduced disulfide bond between residues of the respectiveconstant domains, as described, for example, in WO 2006/000830. TCRs ofthe invention, particularly αβ heterodimeric TCRs, may comprise an αchain TRAC constant domain sequence and/or αβ chain TRBC1 or TRBC2constant domain sequence. The alpha and beta chain constant domainsequences may be modified by truncation or substitution to delete thenative disulfide bond between Cys4 of exon 2 of TRAC and Cys2 of exon 2of TRBC1 or TRBC2. The alpha and/or beta chain constant domainsequence(s) may also be modified by substitution of cysteine residuesfor Thr 48 of TRAC and Ser 57 of TRBC1 or TRBC2, the said cysteinesforming a disulfide bond between the alpha and beta constant domains ofthe TCR. TCRs of the invention may be in single chain format, forexample see WO 2004/033685. In certain embodiments single chain TCRs ofthe invention may have an introduced disulfide bond between residues ofthe respective constant domains, as described in WO 2004/033685.

The invention also provides a cell harbouring a vector of the invention,preferably a TCR expression vector. The vector may comprise nucleic acidof the invention encoding in a single open reading frame, or twodistinct open reading frames, the alpha chain and the beta chainrespectively. Another aspect provides a cell harbouring a firstexpression vector which comprises nucleic acid encoding the alpha chainof a TCR of the invention, and a second expression vector whichcomprises nucleic acid encoding the beta chain of a TCR of theinvention. Such cells are particularly useful in adoptive TCR-T or othercell therapy. The cells may be isolated and/or recombinant and/ornonnaturally occurring and/or engineered.

Since the TCRs of the invention have utility in adoptive TCR-T therapy,the invention includes a nonnaturally occurring and/or purified and/oror engineered cell, especially a T cell, presenting a TCR of theinvention. There are a number of methods suitable for the transfectionof T cells with nucleic acid (such as DNA, cDNA or RNA) encoding theTCRs of the invention (see for example Robbins et al., (2008) J Immunol.180: 6116-6131). T cells expressing the TCRs of the invention will besuitable for use in adoptive therapy-based treatment of cancers such asthose of the pancreas and liver. As will be known to those skilled inthe art, there are a number of suitable methods by which adoptivetherapy can be carried out (see for example Rosenberg et al., (2008) NatRev Cancer 8(4): 299-308). TCR-T cells can be either derived from Tcells in a patient's own blood (autologous) or derived from the T cellsof another healthy donor (allogenic).

As is well-known in the art TCRs of the invention may be subject topost-translational modifications when expressed by transfected cells.Glycosylation is one such modification, which comprises the covalentattachment of oligosaccharide moieties to defined amino acids in the TCRchain. For example, asparagine residues, or serine/threonine residuesare well-known locations for oligosaccharide attachment. Theglycosylation status of a particular protein depends on a number offactors, including protein sequence, protein conformation and theavailability of certain enzymes. Furthermore, glycosylation status (i.eoligosaccharide type, covalent linkage and total number of attachments)can influence protein function. Therefore, when producing recombinantproteins, controlling glycosylation is often desirable. Glycosylation oftransfected TCRs may be controlled by mutations of the transfected gene(Kuball J et al. (2009), J Exp Med 206(2):463-475). Such mutations arealso encompassed in this invention.

Certain TCRs of the invention may be in soluble form (i.e. having notransmembrane or cytoplasmic domains). For stability, TCRs of theinvention, and preferably soluble 13 heterodimeric TCRs, may have anintroduced disulfide bond between residues of the respective constantdomains, as described, for example, in WO 03/020763. Some soluble TCRsof the invention are useful for making fusion proteins which can be usedfor delivering detectable labels or therapeutic agents to antigenpresenting cells and tissues containing antigen presenting cells. Theymay therefore be associated (covalently or otherwise) with a detectablelabel (for diagnostic purposes wherein the TCR is used to detect thepresence of cells presenting peptide:MHC; a therapeutic agent; or apharmacokinetics-modifying moiety (for example by PEGylation).Detectable labels for diagnostic purposes include for instance,fluorescent labels, radiolabels, enzymes, nucleic acid probes andcontrast reagents.

TCRs can be purified from host cells that have been transfected by agene encoding the TCRs by elution of filtered supernatant of host cellculture fluid using a Heparin HP column, using a salt gradient, or othermethods. Fragments or analogs of TCRs can be readily prepared by thoseof ordinary skill in the art following the teachings of thisspecification and using techniques well-known in the art. Preferredamino- and carboxy-termini of fragments or analogs occur near boundariesof functional domains. Structural and functional domains can beidentified by comparison of the nucleotide and/or amino acid sequencedata to public or proprietary sequence databases. Computerizedcomparison methods can be used to identify sequence motifs or predictedprotein conformation domains that occur in other proteins of knownstructure and/or function. Methods to identify protein sequences thatfold into a known three-dimensional structure are known.

In certain embodiments, a TCR comprises one or more water solublepolymer attachments, including, but not limited to, polyethylene glycol,polyoxyethylene glycol, or polypropylene glycol. See, e.g., U.S. Pat.Nos. 4,640,835, 4,496,689, 4,301,144, 4,670,417, 4,791,192 and4,179,337. In certain embodiments, a derivative binding agent comprisesone or more of monomethoxy-polyethylene glycol, dextran, cellulose, orother carbohydrate based polymers, poly-(N-vinylpyrrolidone)-polyethylene glycol, propylene glycol homopolymers, apolypropylene oxide/ethylene oxide co-polymer, polyoxyethylated polyols(e.g., glycerol) and polyvinyl alcohol, as well as mixtures of suchpolymers. In certain embodiments, one or more water-soluble polymer israndomly attached to one or more side chains. In certain embodiments,PEG can act to improve the therapeutic capacity for a binding agent,such as a TCR. Certain such methods are discussed, for example, in U.S.Pat. No. 6,133,426, which is hereby incorporated by reference for anypurpose.

7.6. Methods of Identifying T Cell Receptors

The variable region of TCRα and δ chains is encoded by a number ofvariable (V) and joining (J) genes, while TCRβ and γ chains areadditionally encoded by diversity (D) genes. During VDJ recombination,one random allele of each gene segment is recombined with the others toform a functional variable region. Recombination of the variable regionwith a constant gene segment results in a functional TCR chaintranscript. Additionally, random nucleotides are added and/or deleted atthe junction sites between the gene segments. This process leads tostrong combinatorial (depending on which gene regions will recombine)and junctional diversity (which and how many nucleotides will beadded/deleted), resulting in a large and highly variable TCR repertoire,which will ensure the identification of a plethora of antigens.Additional diversity is achieved by the pairing of α and β or γ and δchains to form a functional TCR.

VDJ recombination of the different TCR genes could theoreticallygenerate between 10¹⁵ and 10²⁰ TCR chains. The actual diversity presentin a human body is estimated at around 10¹³ different clonotypes,implying that the afore-described seemingly random TCR development isobviously not random at all and is subject to different constraints.Moreover, while there are TCRs that are common in the generalpopulation, recent high-resolution studies have shown that the majorityof TCRs is rare (in analogy to common vs. rare genomic variants). Thisis one of the reasons why precise methods are necessary to properlyinvestigate complete individual immune repertoires.

Antibody discovery faces many of the same challenges as TCR discovery,but antibody discovery is far more technologically advanced than TCRdiscovery. For example, methods such as mouse hybridomas (Köhler &Milstein, Nature, 1975, 256(5517):495-7) and phage display (McCaffertyet al., Nature, 1990, 348(6301):552-4) are widely used to quicklyidentify specific and efficacious antibody candidates. Though pioneeringgroups have described methods for yeast display of TCRs (Kieke et al.,PNAS, 1999, 96(10):5651-6), such methods require artificial mutation ofnatural TCRs, which confounds broader utility. Additionally, TCRs arebest studied in the context of T cell surface co-receptors, such as CD8and CD3 (Kuhns et al., Immunity, 2006, 24(2):133-9). Thus, other groupshave reported recombinant expression of TCR libraries in mammalian cells(Chervin et al., Journal of Immunological Methods, 2008, 339(2):175-84;Malecek et al., Journal Immunological Methods, 2013, 392 (1-2):1-11).However, reported technologies fail to leverage the TCR diversity ofnatural human repertoires.

Recently, several groups have described methods that combinemicrofluidics, multiplex PCR, yeast display, and deep sequencing forultra-high-throughput discovery of antibodies from human repertoires(Adler et al., MAbs, 2017, 9(8):1282-1296; Wang et al., NatureBiotechnol, 2018, 36(2):152-155). Here, we report a similar technologyfor ultra-high-throughput discovery of TCRs from human repertoires Humanrepertoires can be virus-positive, healthy donors, cancer donors, donorswith autoimmunity, or donors with any disease condition. Because thediversity of TCRαβ repertoires are generated by millions of single cellsexpressing different TCRα and TCRβ sequences, we first use a dropletmicrofluidic technology to isolate single cells into droplet emulsionsand natively pair TCRα and TCRβ on a single cell level. The microfluidictechnology can process millions of single T cells in an hour, which issignificantly higher throughput than previously reported methods forTCRαβ pairing (Turchaninova et al., Eur Journal of Immunology 2013,43(9):2507-15; Howie et al., Science Translational Medicine 2015,7(301):301ra131). TCRα and TCRβ transcripts are captured from lysedsingle cells, amplified, and then physically linked into a singleamplicon for subsequent cloning into expression vectors. Lysis andamplification are performed in two steps, since the reagents for lysisare incompatible with efficient RT-PCR.

Some other methods are available for natively pairing TCRα and TCRβ viaa single cell barcoding method, for example through a commercial group(10× Genomics; Azizi et al., Cell 2018, 174(5):1293-1308.e36). Singlecells are isolated into microfluidic droplets with molecular barcodes,and then TCRα and TCRβ from the single cells are fused to the uniquebarcodes. The single cell TCRα and TCRβ pairing is then inferred throughbioinformatics. Though these molecular identifiers might offeradvantages in terms of quantification, as used elsewhere for methodsthat do not leverage single cells (Shugay et al., 2014), single cellbarcoding methods do not generate libraries of physically linked TCRαand TCRβ. This complicates any downstream efforts to identify bindingand avidity properties of the TCRαβ sequences.

In our method, the library of millions of physically linked, nativelypaired TCRαβ amplicons is cloned en masse into expression vectors. Thevectors are then subjected to restriction digestion en masse, and a DNAinsert that encodes a TCR constant domain and translational skipsequence is cloned into the library. The full-length TCRαβ libraries arethen packaged into lentiviral constructs and transduced into Jurkatcells that lack endogenous TCRβ expression and which are additionallyengineered to stably express CD8. The resulting TCR-Jurkat librariescomprise natively linked TCRαβ sequences from millions of single Tcells. The TCR-Jurkat libraries are immortal and renewable, enablingmultiple rounds of panning with multiple antigens, using both binding toMHC multimers and activation by artificial antigen-presenting cells(aAPCs).

Similar methods can be applied to T cell repertoires from any animalwith T cells, for example, mouse, rat, dog, cow, rabbit, or horse.

7.7. Sequences

Sequences 1-84, found in the sequence listing submitted with thisapplication, comprise TCR α and β V(D)J polypeptides for the 42 TCRsdescribed in Table 4. For example, TCR 1 comprises SEQ ID NO:1 (TCRα forTCR 1) and SEQ ID NO:2 (TCRβ for TCR 1), TCR 2 comprises SEQ ID NO:3(TCRα for TCR 2) and SEQ ID NO:4 (TCRβ for TCR 2), TCR 3 comprises SEQID NO:5 (TCRα for TCR 3) and SEQ ID NO:6 (TCRβ for TCR 3), and so on.

7.8. Pharmaceutical Compositions

For administration to patients, the TCRs or TCR-T cells of the inventionmay be provided in a pharmaceutical composition together with one ormore pharmaceutically acceptable carriers or excipients. TCR-T cells inaccordance with the invention will usually be supplied as part of asterile, pharmaceutical composition which will normally include apharmaceutically acceptable carrier. This pharmaceutical composition maybe in any suitable form, (depending upon the desired method ofadministering it to a patient). It may be provided in unit dosage form,will generally be provided in a sealed container and may be provided aspart of a kit. Such a kit would normally (although not necessarily)include instructions for use. It may include a plurality of said unitdosage forms. The pharmaceutical composition may be adapted foradministration by any appropriate route, preferably a parenteral(including subcutaneous, intramuscular, or preferably intravenous)route. Such compositions may be prepared by any method known in the artof pharmacy, for example by mixing the active ingredient with thecarriers) or excipient(s) under sterile conditions. TCRs, pharmaceuticalcompositions, vectors, nucleic acids and cells of the invention may beprovided in substantially pure form, for example at least 50%, at least60%, at least 70%, at least 80%, at least 85%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, at least 99% or 100% pure.

Also provided by the invention are: (i) a non-naturally occurring and/orpurified and/or engineered TCR which binds the target peptide:MHC, or acell expressing and/or presenting such a TCR, for use in medicine,preferably in a method of treating cancer. The method may compriseadoptive therapy; (ii) the use of a TCR which binds the targetpeptide:MHC, or a cell expressing and/or presenting such a TCR, in themanufacture of a medicament for treating cancer; (iii) a method oftreating cancer in a patient, comprising administering to the patient aTCR which binds the peptide:MHC target, or a cell expressing and/orpresenting such a TCR. Therapeutic agents which may be associated withthe TCRs of the invention include immunomodulators, radioactivecompounds, enzymes (perforin for example) or chemotherapeutic agents(cis-platin for example). To ensure that toxic effects are exercised inthe desired location the toxin could be inside a liposome linked to aTCR so that the compound is released slowly. This will prevent damagingeffects during the transport in the body and ensure that the toxin hasmaximum effect after binding of the TCR to the relevant antigenpresenting cells.

Other suitable therapeutic agents include small molecule cytotoxicagents, i.e. compounds with the ability to kill mammalian cells having amolecular weight of less than 700 Daltons. Such compounds could alsocontain toxic metals capable of having a cytotoxic effect. Furthermore,it is to be understood that these small molecule cytotoxic agents alsoinclude pro-drugs, i.e. compounds that decay or are converted underphysiological conditions to release cytotoxic agents. Examples of suchagents include cis-platin, maytansine derivatives, rachelmycin,calicheamicin, docetaxel, etoposide, gemcitabine, ifosfamide,irinotecan, melphalan, mitoxantrone, sorfimer sodiumphotofrin II,temozolomide, topotecan, trimetreate glucuronate, auristatin Evincristine and doxorubicin; peptide cytotoxins, i.e. proteins orfragments thereof with the ability to kill mammalian cells. For example,ricin, diphtheria toxin, pseudomonas bacterial exotoxin A, DNase andRNase; radio-nuclides, i.e. unstable isotopes of elements which decaywith the concurrent emission of one or more of a or b particles, or grays. For example, iodine 131, rhenium 186, indium 111, yttrium 90,bismuth 210 and 213, actinium 225 and astatine 213; chelating agents maybe used to facilitate the association of these radio-nuclides to thehigh affinity TCRs, or multimers thereof; immuno-stimulants, i.e. immuneeffector molecules which stimulate immune response. For example,cytokines such as IL-2 and IFN-g, Superantigens and mutants thereof;TCR-HLA fusions; chemokines such as IL-8, platelet factor 4, melanomagrowth stimulatory protein, etc; antibodies or fragments thereof,including anti-T cell or NK cell determinant antibodies (e.g. anti-CD3,anti-CD28 or anti-CD16); alternative protein scaffolds with antibodylike binding characteristics complement activators; xenogeneic proteindomains, allogeneic protein domains, viral/bacterial protein domains,viral/bacterial peptides.

7.9. Methods of Use

Therapeutic TCRs may be used that specifically bind to antigen target ortargets.

In vivo and/or in vitro assays may optionally be employed to helpidentify optimal dosage ranges. The precise dose to be employed in theformulation will also depend on the route of administration, and theseriousness of the condition, and should be decided according to thejudgment of the practitioner and each subject's circumstances. Effectivedoses may be extrapolated from dose-response curves derived from invitro or animal model test systems.

An oligopeptide or polypeptide is within the scope of the invention ifit has an amino acid sequence that is at least 75%, 76%, 77%, 78%, 79%,80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98% or 99% identical to least one of the CDRsprovided herein.

The terms “treatment,” “treating,” and the like are used herein togenerally mean obtaining a desired pharmacologic and/or physiologiceffect. The effect may be prophylactic, in terms of completely orpartially preventing a disease, condition, or symptoms thereof, and/ormay be therapeutic in terms of a partial or complete cure for a diseaseor condition and/or adverse effect, such as a symptom, attributable tothe disease or condition. “Treatment” as used herein covers anytreatment of a disease or condition of a mammal, particularly a human,and includes: (a) preventing the disease or condition from occurring ina subject which may be predisposed to the disease or condition but hasnot yet been diagnosed as having it; (b) inhibiting the disease orcondition (e.g., arresting its development); or (c) relieving thedisease or condition (e.g., causing regression of the disease orcondition, providing improvement in one or more symptoms). Improvementsin any conditions can be readily assessed according to standard methodsand techniques known in the art. The population of subjects treated bythe method of the disease includes subjects suffering from theundesirable condition or disease, as well as subjects at risk fordevelopment of the condition or disease.

By the term “therapeutically effective dose” or “effective amount” ismeant a dose or amount that produces the desired effect for which it isadministered. The exact dose or amount will depend on the purpose of thetreatment, and will be ascertainable by one skilled in the art usingknown techniques (see, e.g., Lloyd (1999) The Art, Science andTechnology of Pharmaceutical Compounding).

The term “sufficient amount” means an amount sufficient to produce adesired effect.

The term “therapeutically effective amount” is an amount that iseffective to ameliorate a symptom of a disease. A therapeuticallyeffective amount can be a “prophylactically effective amount” asprophylaxis can be considered therapy.

The term “ameliorating” refers to any therapeutically beneficial resultin the treatment of a disease state, e.g., a neurodegenerative diseasestate, including prophylaxis, lessening in the severity or progression,remission, or cure thereof.

The actual amount administered, and rate and time-course ofadministration, will depend on the nature and severity of proteinaggregation disease being treated. Prescription of treatment, e.g.decisions on dosage etc., is within the responsibility of generalpractitioners and other medical doctors, and typically takes account ofthe disorder to be treated, the condition of the individual patient, thesite of delivery, the method of administration and other factors knownto practitioners. Examples of the techniques and protocols mentionedabove can be found in Remington's Pharmaceutical Sciences, 16th edition,Osol, A. (ed), 1980.

In some embodiments, the pharmaceutical composition is administered byinhalation, orally, by buccal administration, by sublingualadministration, by injection or by topical application.

In some embodiments, the pharmaceutical composition is administered inan amount sufficient to modulate survival of neurons or dopaminerelease. In some embodiments, the major cannabinoid is administered inan amount less than 1 g, less than 500 mg, less than 100 mg, less than10 mg per dose.

In some embodiments, the pharmaceutical composition is administered oncea day, 2-4 times a day, 2-4 times a week, once a week, or once every twoweeks.

7.10. Examples

Below are examples of specific embodiments for carrying out the presentinvention. The examples are offered for illustrative purposes only, andare not intended to limit the scope of the present invention in any way.Efforts have been made to ensure accuracy with respect to numbers used(e.g., amounts, temperatures, etc.), but some experimental error anddeviation should, of course, be allowed for.

Example 1: Identification of Anti-Viral TCRs from Human Donor T CellRepertoires

Sourcing and Processing Human Materials

De-identified peripheral blood mononuclear cells (PBMCs) in leukopakswere obtained from HLA-A*02:01 and HLA-A*24:02 healthy donors(AllCells), under a protocol approved by an Institutional Review Board(IRB). T cells were isolated from the PBMCs using the Easy Sep™ Human TCell Enrichment Kit (Stemcell Technologies). Following isolation, Tcells were cryopreserved using CryoStor® CS10 (Stemcell Technologies).For downstream single cell TCR□-TCR□ linkage, cells were thawed, washed,and resuspended at 5,000-6,000 cells per □l in cold DPBS+0.5% BSA with12% OptiPrep™ Density Gradient Medium (Sigma). The resuspended cellswere then used for microfluidic encapsulation as described in the nextsection.

Generating Paired TCRα-TCRβ Linkage Libraries

Library generation is divided into three steps: (i) poly(A)+ mRNAcapture, (ii) multiplexed overlap extension reverse transcriptasepolymerase chain reaction (OE-RT-PCR), and (iii) nested PCR to removeartifacts and add adapters for deep sequencing or expression libraries(Adler et al., 2017).

For poly(A)+ mRNA capture, we used a custom designed co-flow emulsiondroplet microfluidic chip fabricated from glass (Dolomite). Themicrofluidic chip has two input channels for fluorocarbon oil(Dolomite), one input channel for the cell suspension mix, and one inputchannel for oligo-dT beads (New England Biolabs) in 0.5M NaCl, 0.5%Tween-20, and 20 mM DTT. The input channels are etched to 50 μm×150 μmfor most of the chip's length, narrow to 55 μm at the droplet junction,and are coated with hydrophobic Pico-Glide (Dolomite). Three MitosP-Pump pressure pumps (Dolomite) are used to pump the liquids throughthe chip. Droplet size depends on pressure, but typically we find thatdroplets of ˜45 μm diameter are optimally stable. Emulsions werecollected into 1.5 mL microcentrifuge tubes and incubated at 40° C. for30 minutes to capture mRNA onto oligo-dT beads. Emulsions were thenbroken using Pico-Break (Dolomite) and mRNA-bound beads are magneticallyisolated.

For multiplex OE-RT-PCR, mRNA-bound beads were re-encasuplated intodroplets with an OE-RT-PCR mix. The OE-RT-PCR mix contains 2× one stepRT-PCR buffer (ThermoFisher), 2.0 mM MgSO4, SuperScript III reversetranscriptase (ThermoFisher), and Platinum Taq (ThermoFisher), plus amixture of primers directed against the TRAC, TRBC, and all V-generegions. TCR□ and TCR□ chains are physically linked by overlappingprimer sequences included on the TRAC and TRBV primers. The amplifiedDNA was recovered from the droplets using a proprietary droplet breakingsolution (GigaMune) and purified using a QIAquick PCR Purification Kit(Qiagen).

For nested PCR, the OE-RT-PCR product was first run on a 1.7% agarosegel and a band at 800-1200 bp was excised and purified using NucleoSpinGel and PCR Clean-up Kit (Macherey-Nagel). Nested PCR was performedusing NEBNext amplification mix (NEB) to add adapters for Illuminasequencing or cloning into a mammalian expression construct. PCRproducts were run on a 1.2% agarose gel, and the 800-1100 bp band wasexcised and purified using NucleoSpin Gel and PCR Clean-up Kit(Macherey-Nagel).

We ran 4 million live T cells from each of our six PBMC donors throughthis workflow to generate our six TCRαβ libraries.

Linked TCRαβ Repertoire Sequencing

Deep TCRαβ sequencing libraries were quantified using a quantitative PCRIllumina Library Quantification Kit (Kapa Biosystems) and diluted to8.5-10 pM. Libraries were sequenced on a MiSeq (Illumina) using v3600-cycle MiSeq Reagent Kits, according to the manufacturer'sinstructions. To identify the paired sequences from the TCRαβ libraries,we obtain forward reads of 357 cycles that cover the TCRα V gene andCDR3, and reverse reads of 162 cycles that cover the TCRβ CDR3 andenough of the TCRβ V gene for accurate calling.

To remove base call errors, we use the expected error filtering methodof Edgar and Flyvbjerg (Edgar, Bioinformatics 2015, 31(21):3476-82). Theexpected number of errors (E) for a read is calculated from its Phredscores. By default, reads with E>1 are discarded, leaving reads forwhich the most probable number of base call errors is zero. For theclonotypes analyzed in this study, we excluded singletons and requiredthat unique CDR3α+CDR3β paired sequences share the same V and J genes.

To identify reading frame and CDR3 amino acid sequences generated byV(D)J rearrangements, we first processed a database of well-curated TCRsequences (IMGT, http://www.imgt.org/download/LIGM-DB/; Lefranc et al.,2009) to generate position-specific sequence matrices (PSSMs) for the 5′and 3′ CDR3 junctions. Each nucleotide sequence from the Illuminasequencing runs was translated into all reading frames. We then used thePSSMs to identify the FR3-CDR3 (5′) and CDR3-FR4 (3′) junctions and theappropriate protein reading frame for each of the nucleotide sequences.To report a CDR3 sequence, we required 5′ and 3′ PSSM hits in the samereading frame. Additionally, sequences that had low PSSM identity scoreswere marked with an exclamation point. These steps allowed us to predictvalid, functional, CDR3 sequences with high confidence. We queried TCRαand TCRβ nucleotide sequences against the IMGT database of reference Vand J gene germline sequences using UBLAST(https://www.drive5.com/usearch/manual/ublast_algo.html; Edgar, 2010); Vand J genes were identified based on the UBLAST alignments with the bestalignment (lowest E-values).

We used our massively parallel single cell droplet and sequencingtechnology to analyze the linked TCRαβ repertoires of three HLA-A*02:01donors and three HLA-A*24:01 donors that were all seropositive for bothcytomegalovirus (CMV) and Epstein-Barr virus (EBV).

Illumina sequencing error can be difficult to differentiate from bonafide TCRαβ sequence diversity (Shugay et al., 2014), so we appliedconservative informatics to eliminate low-quality sequences. If wedefine TCRαβ clonotypes as sequences with unique combinations of CDR3α,CDR3β, and VJ genes, the libraries contained an average of 455,195sequences (range: 339,707 to 721,521), for a total of 2,731,172 TCRαβsequences. If we discard singletons, requiring at least 2 sequencingreads per clonotype, the TCRαβ libraries comprise an average of 141,588TCRαβ sequences (range: 84,871 to 204,426), for a total of 849,525 TCRαβsequences. The TCRαβ libraries were highly diverse, with the medianclonotypes accounting for on average 0.00075% of the total sequencingreads. There were on average 1,912 different Vβ-Vα pairings (range:1,772 to 2,036) in each repertoire. In sum, the repertoires spanned atotal of 2,160 different Vβ-Vα pairings, with a wide range offrequencies.

Single Chain TCRα and TCRβ Repertoire Sequencing

For single chain sequencing of the recombinant TCRα-TCRβ expressionlibraries, TCRα and TCRβ V(D)J regions were amplified separately usinguniversal primers, that contained adapters for Illumina sequencing,within the TRAV.SS and TRAC regions for TCRα and within the TRBV.SS andTRBC regions for TCRβ. We conducted RT-PCR off RNA samples usingSuperScript III reverse transcriptase (ThermoFisher) and Platinum Taq(ThermoFisher). We used NEBNext amplification mix (NEB) for PCR offplasmid DNA. These amplicons were run on 1.7% agarose gels and the500-600 bp band was excised and purified using NucleoSpin Gel and PCRClean-up Kit (Macherey-Nagel). Samples were separately quantified usingan Illumina Library Quantification Kit (Kapa Biosystems). After dilutingto 9 pM, libraries were sequenced on a MiSeq (Illumina) using v2500-cycle MiSeq Reagent Kits, according to the manufacturer'sinstructions. We obtained overlapping forward and reverse reads of 255cycles for TCRα and TCRβ separately. TCRα and TCRβ sequences wereanalyzed separately using the same methods as described above for pairedsequences, with the additional requirement that overlapping reads wereobserved.

Generating Recombinant TCRαβ Jurkat Expression Libraries

We developed a subcloning workflow to convert the linked TCRαβ ampliconsinto full-length lentiviral expression constructs. In this workflow, wefirst used nested PCR to add overhang adapters to the 5′ and 3′ ends ofthe linked TCRαβ amplicons for downstream Gibson assembly. Then, we usedNEBuilder HiFi DNA Assembly Master Mix (New England Biolabs) to insertthe linked TCRαβ library into a pReceiver-based lentiviral vector(GeneCopoeia) that contains the EF1α promoter, a TCRα signal sequence,the TCRβ constant region, and the Puromycin resistance gene. Wetransformed this intermediate library into Endura electrocompetent E.coli (Lucigen), plated onto LB Lennox carbenicillin plates (Teknova),and scraped and pooled >5 million colonies from each library for plasmidpurification. Plasmids were purified using the endotoxin free ZymoPUREII Plasmid Maxiprep Kit (Zymo Research). These intermediate librarieswere linearized with a NheI-HF (New England Biolabs) restriction digestpresent within the linker region, run on a 0.8% agarose gel, and gelextracted using the NucleoSpin Gel and PCR Clean-up Kit(Macherey-Nagel). To create the full-length TCRαβ lentiviral libraries,we performed a second Gibson assembly to insert the TCRα constantregion, a ribosomal skip motif (P2A; Funston, Journal General Virology2008, 89 (Pt 2):389-96), and a TCRβ signal sequence. These full-lengthTCRαβ lentiviral libraries were transformed into Endura electrocompetentcells and purified using the endotoxin free maxiprep kit as describedabove.

Engineering Human CD8 Expressing Jurkat Cells

To screen our natively paired TCRαβ libraries for TCRs reactive toMHC-class I presented peptides, we engineered the TCRβ deficient (ΔTCRβ)Jurkat cell line J.RT3-T3.5 (ATCC TIB-153) to stably express human CD8(Lyons, Cancer Immunol Immunother 2006, 55(9):1142-50). We built alentiviral vector with the PGK promoter driving expression of humanCD8A, a P2A ribosomal skip motif, CD8B(M-1) (Thakral D, et al, J Immunol2008, 180 (10:7431-42), and an IRES—Blasticidin resistance gene cassettein the pReceiver (GeneCopoeia) backbone. Lentivirus was packaged andtransduced into TCRβ deficient Jurkat cells as described below.Blasticidin selection was started on day two post-transduction andcontinued for 14 days to select for stable integration. CD8 surfaceexpression was confirmed by flow cytometry and this CD8+ ΔTCRβ Jurkatcell line was cryopreserved for future use.

Lentiviral Transduction of Jurkat Cells

We then optimized our lentiviral transduction protocol to obtain a lowtransduction efficiency to ensure that we expressed only one TCRαβ pairper cell. We packaged lentivirus into VSV-G pseudotyped lentiviralparticles using the 3^(rd) generation ViraSafe Lentiviral PackagingSystem (Cell Biolabs) and Lenti-Pac 293Ta cells (GeneCopoeia). 21million Lenti-Pac 293Ta cells per 10 cm plate were transfected with 4.3ug pCMV-VSV-G, 4.3 ug pRSV-Rev, 4.3 ug pCgpV, and 4.3 ug of the TCRαβexpression libraries using Lipofectamine 3000 (ThermoFisher) followingthe manufacturer's protocol. Lentiviral supernatant was collected at 48hours post-transfection, spun down at 500 xg for 10 minutes to eliminatecellular debris, and clarified through a 0.45 um syringe filter. RNA wasisolated from fresh lentiviral supernatant using the NucleoSpin RNAVirus kit (Macherey-Nagel) following the manufacturer's protocol. Freshlentiviral supernatant was used to transduce CD8⁺ ΔTCRβ Jurkat cells.Clarified lentiviral supernatant was added at a 1:10 ratio with Jurkatcells in RPMI media with 10% FBS and 8 ug/ml Polybrene (EMD Millipore).Jurkat cells were incubated with lentiviral particles for 6 hours andthen media was exchanged. Two days after viral transduction, Jurkatcells were analyzed for cell surface CD3 and TCRαβ expression to measureviral transduction efficiency. Cells were then cultured for 14 days withpuromycin to select for stable integration and again assessed for CD3and TCRαβ surface expression. To generate the natively paired TCRαβJurkat expression libraries, we transduced 40 million CD8⁺ ΔTCRβ Jurkatand on day 2 observed surface expression on 8-14% of transduced cellscompared to 4% on the parental Jurkat cells. TCRαβ surface increased to42-56% following selection. For monoclonal TCRαβ cell line generation,800,000 CD8+ ΔTCRβ Jurkat cells were transduced and selected withpuromycin for 14 days. CD3 and TCRαβ surface expression was measuredfollowing selection.

Screening Recombinant TCRαβ Jurkat Libraries

We screened the TCRαβ Jurkat libraries with peptide-HLA (pHLA)dextramers (Immudex) targeting common viral antigens from CMV and EBV.We stained 2-5 million CD8+ TCRαβ Jurkat library cells with 10 ul ofAPC-conjugated dextramer at room temperature for 10 minutes. Cells werethen stained with an anti-CD3-FITC antibody (clone: UCHT1; BioLegend)for 30 minutes at 4° C. and DAPI (BioLegend) to assess cell viability.Cells were then sorted on a FACSMelody (BD Biosciences) for LiveCD3⁺/dextramer⁺ cells. The sorted Jurkat cells were recovered andexpanded in RPMI media with 10% FBS and 100 U/ml Pen/Strep (Gibco). Oncecells reached high viability (>85%) and appropriate cell numbers, 2million cells were lysed, and RNA was extracted using the NucleoSpin RNAPlus kit (Macherey-Nagel) for single chain TCRα and TCRβ repertoiresequencing as described above. Multiple rounds of dextramer staining,FACS sorting, and cell expansion were conducted to enrich forpopulations of pHLA-binding TCRs.

Following pHLA-binding enrichment, we co-cultured CD8⁺ TCRαβ Jurkat cellpopulations with peptide-pulsed antigen presenting cells (APCs) toassess cell activation. We pulsed T2 cells with 1004 peptide, mixed200,000 peptide-pulsed T2 cells with 200,000 CD8⁺ TCRαβ Jurkat cells perwell in 96-well round-bottom plates (Falcon), and cultured for 16-20hours. Cells were harvested out of the round-bottom plates and stainedfor HLA-A2 (clone: BB7.2; BioLegend), CD69 (clone: FN50; BioLegend),CD62L (clone: DREG-56; Bio-Legend), and cell viability with DAPI. Cellswere analyzed on a FACSMelody or CytoFLEX LX (Beckman Coulter) foractivation (HLA-A2−/CD69+/CD62L−). We used 1× Cell Stimulation Cocktail(eBioscience, ThermoFisher) as a positive control and irrelevantpeptide-pulsed T2 cells as a negative control. T2 cells natively expressHLA-A*02:01, and we generated a stable T2 cell line that expressesHLA-A*24:02 and GFP (data not shown) for additional peptidepresentation. To identify TCRs present in peptide-activated Jurkatcells, we co-cultured partially enriched TCRαβ Jurkat cell populationswith peptide-pulsed T2 cells, stained with the activation markersdescribed above and sorted for activated (HLA-A2−/CD69+/CD62L−) cells ona FACSMelody. These activated cells were lysed and RNA isolated usingthe NucleoSpin RNA Plus XS kit (Macherey-Nagel) for single chain TCRαand TCRβ repertoire sequencing. Peptides were synthesized at >90% purity(ELIM Biopharm), resuspended in DMSO to 4 mg/ml, aliquoted for singleuse, and stored at −20° C.

To identify virus-specific TCRαβ clones, we stained 2-5 millionTCR-Jurkat cells with fluorescently labeled MHC dextramers against fivewell-characterized peptide:MHC targets: HLA-A*02:01 CMV pp65(NLV),HLA-A*02:01 CMV IE-1(VLE), HLA-A*02:01 EBV BMLF1(GLC), HLA-A*02:01 EBVLMP2(CLG), and HLA-A*24:02 EBV LMP2(TYG). All three of the HLA-A*02:01donors yielded putative binder clones, with Donor CSS-930 yieldingclones against all four HLA-A*02:01 targets. Donor CSS-948 showed someputative binders against HLA-A*24:02 EBV LMP2(TYG). In general, TCRαβclones directed against the peptide:MHC targets were rare, ranging from0.02-0.14% of the cells in the TCR-Jurkat repertoires. In parallel, westained 1-3 million primary PBMC T cells from the same donors and foundsimilar frequencies of virus-specific cells (range: 0.055-0.32%). Unlikeprimary PBMC T cells, Jurkat cells are easy to culture and expandindefinitely. This feature enables us to expand the “Round 1 dextramer”cells, re-stain with dextramer, and sort a second time (“Round 2dextramer”), an approach which we term “panning”, as for phage display(McCafferty et al., 1990). To test the method, we first performedcontrol experiments with a previously reported HLA-A*02:01 human MART-1TCRαβ clone spiked in at a range of 0.001-1% frequencies Panningrecovered the clone quantitatively across all levels tested. We pannedthe six TCR-Jurkat libraries against the five peptide:MHC virus targetsPanning increased oligoclonality considerably, generating top 20 medianclone frequencies of 64.6% after the Round 2 sorts (range: 16.2-21.8%),94.3% after the Round 3 sorts (range: 44.1-88.9%), and 97.1% after theRound 4 sorts (range: 95.4-98.6%). In one case (Donor CSS-944), a singlepp65(NLV) clone comprised >95% of the Round 4 sort.

Because FACS never achieves 100% specificity and 100% sensitivity, weassumed that panning would result in both bona fide and false-positiveTCRαβ clones. TCRαβ clones present a relatively high frequencies in theinitial repertoires are more likely to appear as false positives. Withthis issue in mind, we identified twenty-four TCRαβ clones thatwere >10-fold enriched between the original repertoire and the lastround of panning. The median enrichment for these TCRαβ clones was6,480-fold, with two TCRαβ clones enriched more than one million-fold.The clones were generally very rare in the initial repertoires (median:0.035%), with one TCRαβ clone initially present at 0.000035% of theinitial repertoire.

Therapeutically relevant TCRs should activate T cells upon binding theircognate peptide:MHC, but prior work has established that TCRs can bindtheir peptide:MHC target but fail to activate T cells (Sibener et al.,Cell 2018, 174(3):672-687.e27). Thus, to further reduce false positives,we performed in vitro activation screens on MHC dextramer-enriched TCRαβJurkat populations. Panning Round 2, 3, or 4 TCR-Jurkat populations wereincubated with peptide-pulsed T2 cells, and then FACS-selected forincreased cell surface CD69 and decreased CD62L expression. The ratio ofthe frequency of a TCR in the CD69+/CD62L− fraction to its frequency inthe CD69−/CD62L+ fraction was used to quantify the TCR's ability toactivate T cells. Activation ratios were integrated with correspondingTCRαβ read frequencies after the 3^(rd) or 4^(th) round of MHC dextramerpanning, to assess the likelihood of a true positive. The medianactivation ratio was 0.53, suggesting that the majority of the MHCdextramer-panned TCRs were false positives. However, 10/24 of the TCRαβclones that were highly enriched by MHC dextramer panning also hadactivation ratios of >0.9.

Monoclonal TCRαβ Characterization

Enriched TCRα and TCRβ single chain sequences were identified from thepHLA-binding and cell activation screens. We used this enrichment dataand the natively paired TCRα-TCRβ sequencing data to identify candidateantigen-reactive TCR clones. We designed full-length TCRα-TCRβlentiviral expression constructs using the Illumina sequencing data,specifically the CDR3 nucleotide sequences and V-gene calls, andsynthesized these plasmids using the BioXp 3200 system (SGI-DNA). Thesemonoclonal TCRαβ expression constructs follow the same layout as theTCRαβ libraries. Lentiviral plasmids were sequence verified by Sangersequencing, packaged into VSV-G pseudotyped lentiviral particles,transduced into CD8⁺ ΔTCRβ Jurkat cells, and stable cell lines wereselected.

Monoclonal CD8⁺ TCRαβ Jurkat cell lines were assessed for pHLA bindingand cellular activation. We stained 0.5-1 million cells with 5 ul ofpHLA dextramer and anti-CD3 antibodies as described above. We then ranco-culture assays with the monoclonal CD8⁺ TCRαβ Jurkat cell lines thatshowed pHLA binding. As described above, we pulsed T2 cells with 1004peptide, mixed 200,000 peptide-pulsed T2 cells with 200,000 TCRαβ Jurkatcells per well, and measured cell activation by staining for CD69 andCD62L.

We then measured functional avidity of the monoclonal TCRs that showedcellular activation using T2 cells pulsed with a dilution series ofpeptide (1E-7-10 μM). Cells were co-cultured in duplicate wells for 20hours, harvested, pooled, and stained for activation markers asdescribed above. Cells were run on the CytoFLEX LX and Jurkat cell CD69Median Fluorescence Intensity (MFI) was calculated using FlowJo(Treestar) and analyzed in Prism (GraphPad). Two independent experimentswere conducted, and the mean and standard deviation values were plotted.

Finally, we analyzed a set of antigen-reactive TCRs for peptidespecificity using alanine scanning mutagenesis as previously described(Chheda Z S, Journal of Exp Med 2018, 215(1):141-157). Syntheticpeptides with alanine substitutions were obtained from Pepscan (purity:crude), resuspended in DMSO to 5 mg/ml, aliquoted, and stored at −20° C.T2 cells were pulsed with 10 μg/ml of peptide and co-cultured withmonoclonal CD8⁺ TCRαβ Jurkat cell lines for 24 hours as described above.Following co-culture, cell supernatant was removed and stored at −80° C.IL-2 levels were measured in cell supernatant by sandwich ELISA(BioLegend) following the manufacturer's protocol. MaxiSorp ELISA plateswere coated with antibody at 4° C. overnight. ELISA wells were blockedwith PBS+1% BSA, 50 μl of cell supernatant was added to duplicate wellsand incubated at room temperature for 2 hours, and IL-2 levels weremeasured using an anti-IL-2 detection antibody followed by Avidin-HRPincubation and signal development with aTMB substrate solution. Signalabsorbance was read at 450 nm on a SpectraMax i3× (Molecular Devices).IL-2 levels were calculated using a standard curve run on the sameplate. Two independent experiments were conducted; mean and standarddeviation values were plotted in Prism (GraphPad). Generally, peptideswith alanine mutations induced lower IL-2 secretion than wild typecognate peptides, and irrelevant peptides did not induce IL-2 secretion.The data provided some evidence of contact residues, which variedbetween TCRs and peptide:MHC targets.

TABLE 4 Funtional annotation of TCR sequences Library MonoclonalMonoclonal Target Library Binding Activation Binding Activation TCRnumber A2/pp65(NLV) Yes No No (weak Not tested 1 expression)A2/pp65(NLV) Yes No Yes No 2 A2/pp65(NLV) Yes No No Not tested 3A2/pp65(NLV) Yes No No Not tested 4 A2/pp65(NLV) Enriched but No No Nottested 5 background binding A2/pp65(NLV) Enriched but No No Not tested 6background binding A2/pp65(NLV) Enriched but No No Not tested 7background binding A2/pp65(NLV) Yes Yes Yes Yes 8 A2/pp65(NLV) Yes NoYes No 9 A2/pp65(NLV) Yes Yes Yes No 10 A2/pp65(NLV) No No No Not tested11 A2/pp65(NLV) No No No Not tested 12 A2/pp65(NLV) No No No Not tested13 A2/pp65(NLV) No No No Not tested 14 A2/IE-1(VLE) Yes Yes Yes Yes 15A2/IE-1(VLE) Yes No No Not tested 16 A2/IE-1(VLE) Yes No No (weak Nottested 17 expression) A2/IE-1(VLE) Yes No No Not tested 18 A2/BMLF1(GLC)Yes Yes Yes Yes 19 A2/BMLF1(GLC) Yes No No Not tested 20 A2/BMLF1(GLC)Yes No No Not tested 21 A2/BMLF1(GLC) Yes No No Not tested 22A2/BMLF1(GLC) Yes (weak) No Slight Slight 23 binding activation (weak(weak expression) expression) A2/BMLF1(GLC) Yes Yes Yes (weak) Yes 24A2/BMLF1(GLC) Yes No No Not tested 25 A2/BMLF1(GLC) Yes No No Not tested26 A2/BMLF1(GLC) Enriched but No No (weak Not tested 27 backgroundexpression) binding A2/BMLF1(GLC) Enriched but No No Not tested 28background binding A2/LMP2(CLG) Yes Yes Yes Yes 29 A2/LMP2(CLG) Yes NoNo Not tested 30 A2/LMP2(CLG) Yes No No Not tested 31 A2/LMP2(CLG) YesYes Yes (weak) Yes 32 A2/LMP2(CLG) Yes (weak) No No Not tested 33A2/LMP2(CLG) Yes Yes No No 34 A2/LMP2(CLG) Yes (weak) Yes Yes (weak) Yes35 A2/LMP2(CLG) Yes Yes No No 36 A2/LMP2(CLG) Yes Yes No No 37A24/LMP2(TYG) Yes Target and Yes? (very Yes 40 irrelevant weak) peptideactivated A24/LMP2(TYG) Little to no No No Not tested 41 enrichmentA24/LMP2(TYG) Yes No No Not tested 42

8. INCORPORATION BY REFERENCE

All publications, patents, patent applications and other documents citedin this application are hereby incorporated by reference in theirentireties for all purposes to the same extent as if each individualpublication, patent, patent application or other document wereindividually indicated to be incorporated by reference for all purposes.

9. EQUIVALENTS

Whereas various specific embodiments have been illustrated anddescribed, the above specification is not restrictive. It will beappreciated that various changes can be made without departing from thespirit and scope of the invention(s). Many variations will becomeapparent to those skilled in the art upon review of this specification.

1-9. (canceled)
 10. A method of identifying T cell receptors specific toa target peptide, comprising: providing primary T cells from at leastone human donor; isolating individual primary T cells from the at leastone human donor in droplets; isolating poly(A)+ mRNA transcripts bycapture from the isolated primary T cells; generating by OE-RT-PCR apaired TCRα-TCRβ linkage library comprising linked TCRαβ amplicons fromthe isolated poly(A)+ mRNA transcripts; performing nested PCR;converting said linked TCRαβ amplicons into expression constructs forexpression of full-length TCRαβ; introducing said expression constructsinto a plurality of host cells; inducing expression of recombinant Tcell receptors from said expression constructs in said plurality of hostcells, thereby generating a full-length TCRαβ expression library;exposing the plurality of host cells to peptide-pulsedantigen-presenting cells; selecting a subset of the host cells bydetecting expression of activation markers in the subset of the hostcells; and sequencing transcripts of TCRα and TCRβ isolated from thesubset of the host cells, thereby identifying T cell receptors specificto the target peptide.
 11. The method of claim 10, wherein the targetpeptide is a viral peptide.
 12. The method of claim 10, wherein theactivation markers are selected from the group consisting of CD69 andCD62L.
 13. The method of claim 10, wherein the subset of the host cellsare selected for being CD69+ and CD62L−.
 14. The method of claim 10,wherein the selecting step is performed by cell sorting using theactivation markers.
 15. The method of claim 10, wherein the at least onemammalian donor has been exposed to the virus.
 16. The method of claim10, wherein the virus is CMV or EBV.
 17. The method of claim 10, whereinthe antigen presenting cells are T2 cells.
 18. The method of claim 10,wherein the host cells are CD8+ Jurkat cells.
 19. The method of claim10, wherein the primary immune cells express CD4 or CD8.
 20. The methodof claim 10, wherein the recombinant T cell receptor library comprisesat least 100 unique recombinant T cell receptor expression constructs.21. The method of claim 20, wherein the recombinant T cell receptorlibrary comprises at least 1,000 unique recombinant T cell receptorexpression constructs.